RetrogeneDB ID: retro_ocun_294

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 1:94382207..94382486(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: LIN52
• Ensembl ID: ENSOCUG00000017491
• Aliases: None
• Description: lin-52 homolog (C. elegans) [Source:HGNC Symbol;Acc:19856]

Sequence

>retro_ocun_294
ACAGGACAAGAAGCACCTTTGCTAAGTTTTGAAAAACTTGACCATGACTTGTAAGATCTTTGGTAAGACCTATTATCAGG
TGTCGCTGAATTTACAGCTTTCTTCAATAGTCCTAATACTAGCTCTCCAACCAAACGGATGGCTGAGATAGAGTGTGCTG
ATAGGGACACGCTGAAAAGACTGGGAAGCATCACCATGGCTAATTTGATGGAGAAGTGATGAAGTCCACAGAATCTGGCC
TATCAGCTGGAGCTGAATGAGTCCAGACAGAAGCCCAGG

Alignment

ORF - retro_ocun_294 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.52 %
• Parental protein coverage: 80.17 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TDLEASLLSFEKLDRASPDLWPEQLPGVAEFAASFKSPITSSPPKWMAEIERDDIDMLKELGSLTTANLM
          T..EA.LLSFEKLD....DLW...L.GVAEF.A.F.SP.TSSP.K.MAEIE..D.D.LK.LGS.T.ANLM
Retrocopy TGQEAPLLSFEKLDHDL*DLW*DLLSGVAEFTAFFNSPNTSSPTKRMAEIECADRDTLKRLGSITMANLM

Parental  EKVRGLQNLAYQLGLDESREMTR
          EK....QNLAYQL.L.ESR...R
Retrocopy EK**SPQNLAYQLELNESRQKPR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	3.42 RPM
SRP017611_kidney	0.00 RPM	5.27 RPM
SRP017611_liver	0.00 RPM	0.69 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_294 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_294 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_294 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000002534	1 retrocopy	retro_lafr_1097,
Macropus eugenii	ENSMEUG00000007891	1 retrocopy	retro_meug_286,
Mus musculus	ENSMUSG00000085793	1 retrocopy	retro_mmus_750,
Oryctolagus cuniculus	ENSOCUG00000017491	1 retrocopy	retro_ocun_294 ,
Otolemur garnettii	ENSOGAG00000003009	1 retrocopy	retro_ogar_2580,
Ictidomys tridecemlineatus	ENSSTOG00000008100	1 retrocopy	retro_itri_686,
Tupaia belangeri	ENSTBEG00000005405	1 retrocopy	retro_tbel_388,